The 1999 NCAA Division I-A football season saw Florida State named national champions, defeating Virginia Tech in the BCS Sugar Bowl.
Florida State became the first team in history to start out preseason #1 and remain there through the entire season. Their 12–0 season gave them 109 victories in the '90s, the most for any decade. Virginia Tech also had a remarkable season behind freshman quarterback Michael Vick, who was being touted as college football's best player.
Vick was outshone in the national championship game by Florida State wide receiver Peter Warrick. Warrick had early problems with the law, charged with a misdemeanor he sat out two games early in the season. But he scored three touchdowns in the title game, earning MVP honors.
The BCS adopted a new rule after the previous season, nicknamed the "Kansas State Rule," which stated that any team ranked in the top four in the final BCS poll is assured of an invitation to a BCS bowl game.
Kansas State finished 6th in the BCS standings but again received no BCS bowl invitation, this time being passed over in favor of Michigan (ranked eighth). Kansas State's predicament demonstrated early on the problem of trying to balance historic bowl ties and creating a system which gives top bowl bids to the most deserving teams. In addition, for a second straight season, an undefeated team from outside the BCS Automatic Qualifying conferences (Marshall) went undefeated but did not receive a bid to a BCS bowl game, which illustrated the problem of BCS Non-Automatic Qualifying conference teams being shut out of the BCS bowls.
The NCAA Rules Committee adopted the following changes for the 1999 season:
Holding penalties committed behind the line of scrimmage will be enforced from the previous spot, modifying a 1991 rule that penalized holding (as well as illegal use of hands and clipping) committed behind the scrimmage line from the spot of the foul.
The penalty for intentional grounding was changed from a five-yard penalty from the spot of the foul plus loss-of-down to simply a loss-of-down at the spot of the foul.
Bandannas that are visible are considered illegal equipment.
Offensive teams may not break a huddle with 12 or more players.
Continuing action dead-ball fouls against both teams are disregarded, however any disqualified players must leave the game.